We are analyzing https://link.springer.com/article/10.1186/1471-2105-15-144.

Title:
MOIRAI: a compact workflow system for CAGE analysis | BMC Bioinformatics
Description:
Background Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project but presently there is no software package to perform the essential data processing steps. Results Here we describe MOIRAI, a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. We will describe three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples. Conclusions Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. Availiability The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/ .
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Keywords {🔍}

cage, data, workflow, moirai, analysis, article, reads, pubmed, expression, google, scholar, tools, files, workflows, cas, processing, genome, steps, table, libraries, gene, sequencing, results, users, central, lassmann, samples, carninci, quality, bioinformatics, system, based, output, units, figure, authors, information, full, hayashizaki, mapping, file, sequences, research, software, daub, run, mapped, program, size, access,

Topics {✒️}

fastq/sam/bam sequence reads insertion/deletion error profiles cap-analysis gene expression full size image ultra high-throughput sequencer genome-wide identification adjust analysis workflows/pipelines article download pdf k562 cell line paired-end sequencing data file/directory units represented sequence alignment/map format standardized web-based mechanism open access license quality control purposes transcriptome cap analysis unamplified cap analysis privacy choices/manage cookies quality control units quality control programs net/projects/moirai/ tab delimited table transparent computational research timo lassmann generation sequencing data encode cage libraries authors’ original file author information authors measured rna molecules displaying final products references kanamori-katayama related subjects improve sequencing capacity intermediate sequence files annotation pipeline based transcriptional start site annotation files hierarchically central role enable accurate comparison low quality bases comparing genomic features obtained gene models unexpected transcriptional complexity 100bp downstream categories full access mapping rate higher cage profiling nano-cage [7] datasets text/image file demultiplex cage libraries

Schema {🗺️}

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         description:Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project but presently there is no software package to perform the essential data processing steps. Here we describe MOIRAI, a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. We will describe three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples. Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/ .
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      headline:MOIRAI: a compact workflow system for CAGE analysis
      description:Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project but presently there is no software package to perform the essential data processing steps. Here we describe MOIRAI, a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. We will describe three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples. Due to the many built in quality control features MOIRAI is especially suitable to support the development of new sequencing based protocols. The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/ .
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         Pipeline
         Next generation sequencing
         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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